The T cell receptor (TCR) repertoire expressed in mice of different genetic origins was analyzed by flow cytometry and by analysis of TCR-specific mRNA. When TCR V-beta usage was assessed, strain-specific decreases were detected in expression of 12 of the 22 known mouse V-beta products. In each case studied, V-beta deletion was dominant in Fl mice bred between high and low expressors, indicating that these deletions represent negative selection of potentially self-reactive T cells in mice expressing the corresponding self ligands. These V-beta deletions fail to occur in athymic nude mice, demonstrating that the thymus is critical in mediating self tolerance by negative selection. The self ligands mediating V-beta-specific negative selection were analyzed. In most instances, both major histocompatibility complex (MHC)-encoded and non-MHC-encoded components of the deleting ligand were identified. In some instances, the deleting ligand corresponded to a known endogenous superantigen, for example in the demonstration that Mlsc is the ligand for V-beta3-expressing T cells. In other instances, previously unknown superantigens were identified on the basis of observed V-beta deletions, e.g. the demonstration of Mlsf as the ligand for V-betall- and V-betal2-expressing T cells. In several cases, a novel "genetic redundancy', was identified in the non-MHC ligands for V-beta deletion, such that any one of two or more unlinked genes was permissive for deletion. Analysis of TCR V-beta expression has been used to characterize the in vivo response of mice to syngeneic tumors. A non-random but nevertheless highly heterogeneous T cell response was observed in tumor-infiltrating lymphocytes.